I don't live in the Savannah area nor even in GA, so I can't comment intelligently about the SEGARRN system with any expertise. However, I'm across the state line in South Carolina, and I can give you some insight into how SC manages its statewide system known as Palmetto 800
Palmetto 800 is operated by Motorola Systems (the manufacturer of the equipment) on a contract from the state of South Carolina. That contract is administered by the South Carolina Department of Technology, a division of SC Department of Administration. However, the system's operation is governed by a committee of of its users - state, county and local agency communication managers. It's a very unique arrangement.
From an FCC licensing standpoint, many frequencies used for sites are licensed by the State (SC DOA or SC DTO). Most sites with licenses from the state are in locations that don't have a large number of county or local agencies using the system, and so those sites are there to provide coverage for state agencies or local agencies that don't have their own communications operations. Other sites are licensed by the County or local agency they are in. In some cases this was because a county had operated its own separate trunked radio system in the past and at some point chose to "merge" their system with the state's system. In others, the County or agency may have chosen to donate newly licensed frequencies to the state for use by the state system. There are 2 compelling reasons for doing this: one reason is the State may provide some credit on service costs to a county or agency that donates frequencies to be shared by all users on the system. Another is f the county or agency chooses to implement their own system at a later time, they already own frequencies that can be used for that purpose. In any case, the operator (in Palmetto 800's case, Motorola) does not own any licenses used by the system. If the state were to choose a different operator at some point in the future, they and the member agencies still own the frequencies used by whatever system they might implement.
As for determining which frequencies are used by the system and therefore comprises the listing in the RR database, in the case of Palmetto 800 that information is gathered and verified by radio hobbyists using some form of trunked system decoding software. I recall in the late 1990's as I was just beginning to delve into trunk-tracking scanners, I made a data slicer circuit from parts at RadioShack and installed a discriminator tap in one of my scanners and ran the program "trunker" on our local trunked radio site to gather data. This was before online FCC records and the existence of RadioReference, where radio information is easily obtained. I was shocked as I traveled over time through the state when I realized that the system ID of the different trunked radio systems was the same as the one used in my home county. I gradually pieced together information I found online as well as information I gathered on my own and began to understand these relationships. The FCC data is one tool that hobbyists can use to determine potential frequencies. But actual data gathering is what generates most if not all of the listings in the RadioReference database. Keep in mind that not all such systems listed in the RadioReference database are complete or accurate - the data here is only as good as what hobbyists submit to it.
As for frequencies that are licensed but not used, there can be many explanations. In my home county, for example, one frequency licensed as a a part of a local trunked site was actually used as a conventional frequency for paging EMS units. Before commercial wireless data services (aka "cell phone companies") could provide mobile broadband, public safety data systems (mobile data terminals in vehicles) used LMR frequencies. And, as you mentioned, SC also has a network of conventional radio repeaters for interoperability and as a back-up for the statewide trunked system.
Hope that helps with some of your questions.